From 68381f880ac18171246417b6dfc9c35a77d12232 Mon Sep 17 00:00:00 2001
From: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Date: Thu, 1 Dec 2022 23:00:48 +0100
Subject: sci-biology/mRNAmarkup: treeclean

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
---
 sci-biology/mRNAmarkup/Manifest                    |  1 -
 sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild | 55 ----------------------
 sci-biology/mRNAmarkup/metadata.xml                | 12 -----
 3 files changed, 68 deletions(-)
 delete mode 100644 sci-biology/mRNAmarkup/Manifest
 delete mode 100644 sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild
 delete mode 100644 sci-biology/mRNAmarkup/metadata.xml

diff --git a/sci-biology/mRNAmarkup/Manifest b/sci-biology/mRNAmarkup/Manifest
deleted file mode 100644
index fb61347b3..000000000
--- a/sci-biology/mRNAmarkup/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mRNAmarkup-5-21-2019.tar.gz 192535480 BLAKE2B 5aa385ddae79f2d18649ab70ac2939a478714abd84a59621d852888e9f7df4fd666baea8b8e905756a0f259471a35c6ca1fb5f7c2fa7a50769b4cf7c32dd431b SHA512 c05b685db7992e6278b56b34ad4e77c1f1c4bfb5b9f4880062fa07b5674272e5b950480bbfdd5cbfc037e6b87c10544d0fc67a8b55370037649203ce1c730d2a
diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild
deleted file mode 100644
index fb37b69f9..000000000
--- a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Transcript annotation workflow"
-HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php"
-SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-${PV//./-}.tar.gz" # 184MB
-
-LICENSE="mRNAmarkup"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
-	sci-biology/ncbi-tools++
-	sci-biology/estscan"
-# sci-biology/MuSeqBox has fetch-restrict and probably only works with old BLAST plaintex output
-# but, mRNAmarkup/INSTALL says:
-# 'For convenience, a copy of the MuSeqBox code distribution is included in directory src/contributed
-#
-# has a slightly modified estscan copy in src/contributed
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare(){
-	default
-	sed -e \
-		"s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \
-		-i bin/mRNAmarkup.orig || die
-	sed -e \
-		"s#$installdir/bin/ESTScan.conf#/usr/share/mRNAmarkup/etc/ESTScan.conf#" \
-		-i bin/mRNAmarkup.orig
-}
-
-src_compile(){
-	cd src
-	emake
-}
-
-src_install(){
-	mv bin/mRNAmarkup.orig bin/mRNAmarkup
-	sed -e 's#INSTALLDIR#/usr/share/mRNAmarkup/etc/#' -i bin/mRNAmarkup
-	dobin bin/mRNAmarkup bin/*.pl bin/dnatopro bin/genestat
-	# TODO: there are some more files in bin/ , sigh!
-	insinto /usr/share/mRNAmarkup/etc
-	mv mRNAmarkup.conf.orig mRNAmarkup.conf
-	doins mRNAmarkup.conf
-	doins bin/ESTScan.conf
-	dodoc 0README INSTALL
-}
-
-pkg_postinst(){
-	einfo "Please obtain a local copy of NCBI CDD dastabase"
-}
diff --git a/sci-biology/mRNAmarkup/metadata.xml b/sci-biology/mRNAmarkup/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/mRNAmarkup/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
-- 
cgit v1.2.3-65-gdbad